Merge pull request #263 from sbmlteam/remove-robin-from-spatial

Remove the three 'Robin' boundary conditions.
sbmlteam · Aug 8, 2022 · f5788b4 · f5788b4
2 parents 00eb881 + 7abc2cc
commit f5788b4
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Showing 24 changed files with 12 additions and 1,612 deletions.
diff --git a/src/sbml/packages/spatial/extension/SpatialExtension.cpp b/src/sbml/packages/spatial/extension/SpatialExtension.cpp
@@ -465,10 +465,7 @@ SpatialExtension::init()
 static
 const char* SBML_BOUNDARY_KIND_STRINGS[] =
 {
-  "Robin_valueCoefficient"
-, "Robin_inwardNormalGradientCoefficient"
-, "Robin_sum"
-, "Neumann"
+  "Neumann"
 , "Dirichlet"
 , "invalid BoundaryKind value"
 };
@@ -481,7 +478,7 @@ LIBSBML_EXTERN
 const char*
 BoundaryKind_toString(BoundaryKind_t bk)
 {
-  int min = SPATIAL_BOUNDARYKIND_ROBIN_VALUE_COEFFICIENT;
+  int min = SPATIAL_BOUNDARYKIND_NEUMANN;
   int max = SPATIAL_BOUNDARYKIND_INVALID;
 
   if (bk < min || bk > max)
@@ -533,7 +530,7 @@ LIBSBML_EXTERN
 int
 BoundaryKind_isValid(BoundaryKind_t bk)
 {
-  int min = SPATIAL_BOUNDARYKIND_ROBIN_VALUE_COEFFICIENT;
+  int min = SPATIAL_BOUNDARYKIND_NEUMANN;
   int max = SPATIAL_BOUNDARYKIND_INVALID;
 
   if (bk < min || bk >= max)

diff --git a/src/sbml/packages/spatial/extension/SpatialExtension.h b/src/sbml/packages/spatial/extension/SpatialExtension.h
@@ -434,10 +434,7 @@ typedef enum
  */
 typedef enum
 {
-  SPATIAL_BOUNDARYKIND_ROBIN_VALUE_COEFFICIENT                        /*!< The spatial boundarykind is @c "Robin_valueCoefficient". */
-, SPATIAL_BOUNDARYKIND_ROBIN_INWARD_NORMAL_GRADIENT_COEFFICIENT       /*!< The spatial boundarykind is @c "Robin_inwardNormalGradientCoefficient". */
-, SPATIAL_BOUNDARYKIND_ROBIN_SUM                                      /*!< The spatial boundarykind is @c "Robin_sum". */
-, SPATIAL_BOUNDARYKIND_NEUMANN                                        /*!< The spatial boundarykind is @c "Neumann". */
+  SPATIAL_BOUNDARYKIND_NEUMANN                                        /*!< The spatial boundarykind is @c "Neumann". */
 , SPATIAL_BOUNDARYKIND_DIRICHLET                                      /*!< The spatial boundarykind is @c "Dirichlet". */
 , SPATIAL_BOUNDARYKIND_INVALID                                        /*!< Invalid BoundaryKind value. */
 } BoundaryKind_t;
@@ -449,9 +446,6 @@ typedef enum
  * @param bk the #BoundaryKind_t enumeration value to convert.
  *
  * @return A string corresponding to the given type:
- * "Robin_valueCoefficient",
- * "Robin_inwardNormalGradientCoefficient",
- * "Robin_sum",
  * "Neumann",
  * "Dirichlet",
  * or @c NULL if the value is @sbmlconstant{SPATIAL_BOUNDARYKIND_INVALID,
@@ -485,9 +479,9 @@ BoundaryKind_parse(const char* code);
  * @sbmlconstant{SPATIAL_BOUNDARYKIND_INVALID, BoundaryKind_t} if no match is
  * found.
  *
- * @note The matching is case-sensitive: "Robin_valueCoefficient" will return
- * @sbmlconstant{SPATIAL_BOUNDARYKIND_ROBIN_VALUE_COEFFICIENT, BoundaryKind_t},
- * but "Robin_valueCoefficient" will return
+ * @note The matching is case-sensitive: "Neumann" will return
+ * @sbmlconstant{SPATIAL_BOUNDARYKIND_NEUMANN, BoundaryKind_t},
+ * but "neumann" will return
  * @sbmlconstant{SPATIAL_BOUNDARYKIND_INVALID, BoundaryKind_t}.
  *
  * @if conly
@@ -506,10 +500,6 @@ BoundaryKind_fromString(const char* code);
  * @param bk the #BoundaryKind_t enumeration to query.
  *
  * @return @c 1 (true) if the #BoundaryKind_t is
- * @sbmlconstant{SPATIAL_BOUNDARYKIND_ROBIN_VALUE_COEFFICIENT, BoundaryKind_t},
- * @sbmlconstant{SPATIAL_BOUNDARYKIND_ROBIN_INWARD_NORMAL_GRADIENT_COEFFICIENT,
- * BoundaryKind_t},
- * @sbmlconstant{SPATIAL_BOUNDARYKIND_ROBIN_SUM, BoundaryKind_t},
  * @sbmlconstant{SPATIAL_BOUNDARYKIND_NEUMANN, BoundaryKind_t}, or
  * @sbmlconstant{SPATIAL_BOUNDARYKIND_DIRICHLET, BoundaryKind_t};
  * @c 0 (false) otherwise (including
@@ -531,16 +521,13 @@ BoundaryKind_isValid(BoundaryKind_t bk);
  * @param code the string to query.
  *
  * @return @c 1 (true) if the string is
- * "Robin_valueCoefficient",
- * "Robin_inwardNormalGradientCoefficient",
- * "Robin_sum",
  * "Neumann",
  * "Dirichlet", or
  * "invalid BoundaryKind value";
  * @c 0 (false) otherwise.
  *
- * @note The matching is case-sensitive: "Robin_valueCoefficient" will return
- * @c 1 (true), but "Robin_valueCoefficient" will return @c 0 (false).
+ * @note The matching is case-sensitive: "Neumann" will return
+ * @c 1 (true), but "neumann" will return @c 0 (false).
  *
  * @if conly
  * @memberof Spatial_t

diff --git a/src/sbml/packages/spatial/sbml/BoundaryCondition.h b/src/sbml/packages/spatial/sbml/BoundaryCondition.h
@@ -62,12 +62,6 @@
  * Level&nbsp;3 Version&nbsp;1 Spatial specification, the following are the
  * allowable values for "type":
  * <ul>
- * <li> @c "Robin_valueCoefficient", TODO:add description
- *
- * <li> @c "Robin_inwardNormalGradientCoefficient", TODO:add description
- *
- * <li> @c "Robin_sum", TODO:add description
- *
  * <li> @c "Neumann", TODO:add description
  *
  * <li> @c "Dirichlet", TODO:add description
@@ -198,11 +192,6 @@ class LIBSBML_EXTERN BoundaryCondition : public SBase
    * @if clike The value is drawn from the enumeration @ref BoundaryKind_t
    * @endif
    * The possible values returned by this method are:
-   * @li @sbmlconstant{SPATIAL_BOUNDARYKIND_ROBIN_VALUE_COEFFICIENT,
-   * BoundaryKind_t}
-   * @li @sbmlconstant{SPATIAL_BOUNDARYKIND_ROBIN_INWARD_NORMAL_GRADIENT_COEFFICIENT,
-   * BoundaryKind_t}
-   * @li @sbmlconstant{SPATIAL_BOUNDARYKIND_ROBIN_SUM, BoundaryKind_t}
    * @li @sbmlconstant{SPATIAL_BOUNDARYKIND_NEUMANN, BoundaryKind_t}
    * @li @sbmlconstant{SPATIAL_BOUNDARYKIND_DIRICHLET, BoundaryKind_t}
    * @li @sbmlconstant{SPATIAL_BOUNDARYKIND_INVALID, BoundaryKind_t}
@@ -218,9 +207,6 @@ class LIBSBML_EXTERN BoundaryCondition : public SBase
    *
    * @copydetails doc_boundarycondition_type
    * The possible values returned by this method are:
-   * @li @c "Robin_valueCoefficient"
-   * @li @c "Robin_inwardNormalGradientCoefficient"
-   * @li @c "Robin_sum"
    * @li @c "Neumann"
    * @li @c "Dirichlet"
    * @li @c "invalid BoundaryKind value"
@@ -888,11 +874,6 @@ BoundaryCondition_getVariable(const BoundaryCondition_t * bc);
  * @copydetails doc_boundarycondition_type
  * @if clike The value is drawn from the enumeration @ref BoundaryKind_t @endif
  * The possible values returned by this method are:
- * @li @sbmlconstant{SPATIAL_BOUNDARYKIND_ROBIN_VALUE_COEFFICIENT,
- * BoundaryKind_t}
- * @li @sbmlconstant{SPATIAL_BOUNDARYKIND_ROBIN_INWARD_NORMAL_GRADIENT_COEFFICIENT,
- * BoundaryKind_t}
- * @li @sbmlconstant{SPATIAL_BOUNDARYKIND_ROBIN_SUM, BoundaryKind_t}
  * @li @sbmlconstant{SPATIAL_BOUNDARYKIND_NEUMANN, BoundaryKind_t}
  * @li @sbmlconstant{SPATIAL_BOUNDARYKIND_DIRICHLET, BoundaryKind_t}
  * @li @sbmlconstant{SPATIAL_BOUNDARYKIND_INVALID, BoundaryKind_t}
@@ -916,9 +897,6 @@ BoundaryCondition_getType(const BoundaryCondition_t * bc);
  *
  * @copydetails doc_boundarycondition_type
  * The possible values returned by this method are:
- * @li @c "Robin_valueCoefficient"
- * @li @c "Robin_inwardNormalGradientCoefficient"
- * @li @c "Robin_sum"
  * @li @c "Neumann"
  * @li @c "Dirichlet"
  * @li @c "invalid BoundaryKind value"

diff --git a/src/sbml/packages/spatial/validator/SpatialSBMLError.h b/src/sbml/packages/spatial/validator/SpatialSBMLError.h
@@ -345,9 +345,6 @@ typedef enum
 , SpatialBoundaryConditionsMustBeUnique                       = 1223651
 , SpatialDirichletUnits                                       = 1223652
 , SpatialNeumannUnits                                         = 1223653
-, SpatialRobinValueCoefficientUnits                           = 1223654
-, SpatialInwardNormalGradientCoefficientUnits                 = 1223655
-, SpatialRobinSumUnits                                        = 1223656
 , SpatialGeometryAllowedCoreAttributes                        = 1223701
 , SpatialGeometryAllowedCoreElements                          = 1223702
 , SpatialGeometryAllowedAttributes                            = 1223703

diff --git a/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h b/src/sbml/packages/spatial/validator/SpatialSBMLErrorTable.h
@@ -3204,8 +3204,7 @@ static const packageErrorTableEntry spatialErrorTable[] =
     "The value of the attribute 'spatial:type' of a <boundaryCondition> object "
     "must conform to the syntax of SBML data type 'BoundaryKind' and may only "
     "take on the allowed values of 'BoundaryKind' defined in SBML; that is, the "
-    "value must be one of the following: 'Robin_valueCoefficient', "
-    "'Robin_inwardNormalGradientCoefficient', 'Robin_sum', 'Neumann' or "
+    "value must be one of the following: 'Neumann' or "
     "'Dirichlet'.",
     { "L3V1 Spatial V1 Section"
     }
@@ -3250,7 +3249,7 @@ static const packageErrorTableEntry spatialErrorTable[] =
     "Each BoundaryCondition must define only one boundary.",
     LIBSBML_CAT_GENERAL_CONSISTENCY,
     LIBSBML_SEV_ERROR,
-    "For every combination of species and boundary, there must be at most exactly one <boundaryCondition> of type 'Neumann', or exactly one <boundaryCondition> of type 'Dirichlet', or exactly three <boundaryCondition> elements, one of each of the three 'Robin' types.",
+    "For every combination of species and boundary, there must be at most exactly one <boundaryCondition> of type 'Neumann', or exactly one <boundaryCondition> of type 'Dirichlet'.",
     { "L3V1 Spatial V1 Section"
     }
   },
@@ -3275,36 +3274,6 @@ static const packageErrorTableEntry spatialErrorTable[] =
     }
   },
 
-  // 1223654
-  { SpatialRobinValueCoefficientUnits,
-    "A 'Robin_valueCoefficient' BoundaryCondition's units should scale with dimensionless.",
-    LIBSBML_CAT_UNITS_CONSISTENCY,
-    LIBSBML_SEV_WARNING,
-    "The units of a <parameter> with a <boundaryCondition> child of type 'Robin_valueCoefficient' should should scale with the other 'Robin' boundary conditions for the same species and boundary, with suggested base units of dimensionless.",
-    { "L3V1 Spatial V1 Section"
-    }
-  },
-
-  // 1223655
-  { SpatialInwardNormalGradientCoefficientUnits,
-    "A 'Robin_inwardNormalGradientCoefficient' BoundaryCondition's units should scale with 1/length.",
-    LIBSBML_CAT_UNITS_CONSISTENCY,
-    LIBSBML_SEV_WARNING,
-    "The units of a <parameter> with a <boundaryCondition> child of type 'Robin_inwardNormalGradientCoefficient' should should scale with the other 'Robin' boundary conditions for the same species and boundary, with suggested base units of 1/length.",
-    { "L3V1 Spatial V1 Section"
-    }
-  },
-
-  // 1223656
-  { SpatialRobinSumUnits,
-    "A 'Robin_sum' BoundaryCondition's units should scale with concentration.",
-    LIBSBML_CAT_UNITS_CONSISTENCY,
-    LIBSBML_SEV_WARNING,
-    "The units of a <parameter> with a <boundaryCondition> child of type 'Robin_sum' should should scale with the other 'Robin' boundary conditions for the same species and boundary, with suggested base units of the concentration of the referenced <species>.",
-    { "L3V1 Spatial V1 Section"
-    }
-  },
-
   // 1223701
   { SpatialGeometryAllowedCoreAttributes,
     "Core attributes allowed on <geometry>.",

diff --git a/src/sbml/packages/spatial/validator/SpatialUniqueBoundaryConditionsCheck.cpp b/src/sbml/packages/spatial/validator/SpatialUniqueBoundaryConditionsCheck.cpp
@@ -81,7 +81,7 @@ SpatialUniqueBoundaryConditionsCheck::check_(const Model& m, const Model&)
   if (m.getLevel() < 3) {
     return;
   }
-  set<pair<string, string> > dirichlet_targets, neumann_targets, robin_in_targets, robin_value_targets, robin_sum_targets;
+  set<pair<string, string> > dirichlet_targets, neumann_targets;
   for (unsigned long p = 0; p < m.getNumParameters(); p++) {
     const Parameter* param = m.getParameter(p);
     const SpatialParameterPlugin* spp = static_cast<const SpatialParameterPlugin*>(param->getPlugin("spatial"));
@@ -127,27 +127,6 @@ SpatialUniqueBoundaryConditionsCheck::check_(const Model& m, const Model&)
         logFailure(m);
         continue;
       }
-      if (robin_in_targets.find(bc_pair) != robin_in_targets.end()) {
-        if (bk != SPATIAL_BOUNDARYKIND_ROBIN_SUM && bk != SPATIAL_BOUNDARYKIND_ROBIN_VALUE_COEFFICIENT) {
-          msg += ", but another <boundaryCondition> of type 'Robin_inwardNormalGradientCoefficient' already exists for that species boundary.";
-          logFailure(m);
-          continue;
-        }
-      }
-      if (robin_value_targets.find(bc_pair) != robin_value_targets.end()) {
-        if (bk != SPATIAL_BOUNDARYKIND_ROBIN_SUM && bk != SPATIAL_BOUNDARYKIND_ROBIN_INWARD_NORMAL_GRADIENT_COEFFICIENT) {
-          msg += ", but another <boundaryCondition> of type 'Robin_valueCoefficient' already exists for that species boundary.";
-          logFailure(m);
-          continue;
-        }
-      }
-      if (robin_sum_targets.find(bc_pair) != robin_sum_targets.end()) {
-        if (bk != SPATIAL_BOUNDARYKIND_ROBIN_INWARD_NORMAL_GRADIENT_COEFFICIENT && bk != SPATIAL_BOUNDARYKIND_ROBIN_VALUE_COEFFICIENT) {
-          msg += ", but another <boundaryCondition> of type 'Robin_sum' already exists for that species boundary.";
-          logFailure(m);
-          continue;
-        }
-      }
 
 
       switch (bk) {
@@ -157,70 +136,9 @@ SpatialUniqueBoundaryConditionsCheck::check_(const Model& m, const Model&)
       case SPATIAL_BOUNDARYKIND_NEUMANN:
         neumann_targets.insert(bc_pair);
         break;
-      case SPATIAL_BOUNDARYKIND_ROBIN_INWARD_NORMAL_GRADIENT_COEFFICIENT:
-        robin_in_targets.insert(bc_pair);
-        break;
-      case SPATIAL_BOUNDARYKIND_ROBIN_SUM:
-        robin_sum_targets.insert(bc_pair);
-        break;
-      case SPATIAL_BOUNDARYKIND_ROBIN_VALUE_COEFFICIENT:
-        robin_value_targets.insert(bc_pair);
-        break;
       }
     }
   }
-
-  //Now check for exactly three Robin boundaries:
-  for (set<pair<string, string> >::iterator r_i_pair = robin_in_targets.begin(); r_i_pair != robin_in_targets.end(); r_i_pair++) {
-    pair<string, string> rip = *r_i_pair;
-    string msg1 = "A <boundaryCondition> has a variable of '";
-    msg1 += rip.first + "' and a target of '" + rip.second;
-    msg1 += "', with a type of 'Robin_inwardNormalGradientCoefficient', but there is no corresponding <boundaryCondition> with the same variable and target with type '";
-    if (robin_sum_targets.find(rip) == robin_sum_targets.end()) {
-      msg = msg1 + "Robin_sum'.";
-      logFailure(m);
-      robin_sum_targets.insert(rip);
-    }
-    if (robin_value_targets.find(rip) == robin_value_targets.end()) {
-      msg = msg1 + "Robin_valueCoefficient'.";
-      logFailure(m);
-      robin_value_targets.insert(rip);
-    }
-  }
-
-  for (set<pair<string, string> >::iterator r_i_pair = robin_sum_targets.begin(); r_i_pair != robin_sum_targets.end(); r_i_pair++) {
-    pair<string, string> rip = *r_i_pair;
-    string msg1 = "A <boundaryCondition> has a variable of '";
-    msg1 += rip.first + "' and a target of '" + rip.second;
-    msg1 += "', with a type of 'Robin_sum', but there is no corresponding <boundaryCondition> with the same variable and target with type '";
-    if (robin_in_targets.find(rip) == robin_in_targets.end()) {
-      msg = msg1 + "Robin_inwardNormalGradientCoefficient'.";
-      logFailure(m);
-      robin_in_targets.insert(rip);
-    }
-    if (robin_value_targets.find(rip) == robin_value_targets.end()) {
-      msg = msg1 + "Robin_valueCoefficient'.";
-      logFailure(m);
-      robin_value_targets.insert(rip);
-    }
-  }
-
-  for (set<pair<string, string> >::iterator r_i_pair = robin_value_targets.begin(); r_i_pair != robin_value_targets.end(); r_i_pair++) {
-    pair<string, string> rip = *r_i_pair;
-    string msg1 = "A <boundaryCondition> has a variable of '";
-    msg1 += rip.first + "' and a target of '" + rip.second;
-    msg1 += "', with a type of 'Robin_valueCoefficient', but there is no corresponding <boundaryCondition> with the same variable and target with type '";
-    if (robin_in_targets.find(rip) == robin_in_targets.end()) {
-      msg = msg1 + "Robin_inwardNormalGradientCoefficient'.";
-      logFailure(m);
-      robin_in_targets.insert(rip);
-    }
-    if (robin_sum_targets.find(rip) == robin_sum_targets.end()) {
-      msg = msg1 + "Robin_sum'.";
-      logFailure(m);
-      robin_sum_targets.insert(rip);
-    }
-  }
 }